› 4erp

X-ray diffraction
4.45Å resolution

Crystal structure of a gemcitabine-diphosphate inhibited E. coli class Ia ribonucleotide reductase complex

Released:
DOI: 10.2210/pdb4erp/pdb
PDB entry 4erp coloured by chain, front view.
PDB entry 4erp coloured by chain, side view.
PDB entry 4erp coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Tangled up in knots: structures of inactivated forms of E. coli class Ia ribonucleotide reductase.
Zimanyi CM, Ando N, Brignole EJ, Asturias FJ, Stubbe J, Drennan CL
Structure 20 1374-83 (2012)
PMID: 22727814

Function and Biology Details

Reaction catalysed: 
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O = ribonucleoside diphosphate + thioredoxin
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero octamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-132531 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Ribonucleoside-diphosphate reductase 1 subunit alpha Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 761 amino acids
Theoretical weight: 85.88 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P00452 (Residues: 1-761; Coverage: 100%)
Gene names: JW2228, b2234, dnaF, nrdA
Sequence domains:
Ribonucleoside-diphosphate reductase 1 subunit beta Chains: E, F, G, H
Molecule details ›
Chains: E, F, G, H
Length: 375 amino acids
Theoretical weight: 43.43 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P69924 (Residues: 2-376; Coverage: 100%)
Gene names: JW2229, b2235, ftsB, nrdB
Sequence domains: Ribonucleotide reductase, small chain

Ligands and Environments

2 bound ligands:
Ligand ATP 4 x ATP
Ligand FEO 4 x FEO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CHESS BEAMLINE A1
Spacegroup: C2221
Unit cell:
a: 128.669Å b: 398.906Å c: 319.437Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.233 0.233 0.267
Expression system: Escherichia coli

Quick links

Citations

8 review citations

Natural supramolecular protein assemblies.
Pieters et al. (2016)
7 more

1 mention without citation

Tangled up in knots: structures of inactivated forms of E. coli class Ia ribonucleotide reductase.
Zimanyi et al. (2012)